set(alignment_header_files
        alignment/Alignment.h
        alignment/CompressedA3M.h
        alignment/EvalueComputation.h
        alignment/Matcher.h
        alignment/MsaFilter.h
        alignment/MultipleAlignment.h
        alignment/PSSMCalculator.h
        alignment/PSSMMasker.h
        alignment/StripedSmithWaterman.h
        alignment/BandedNucleotideAligner.h
        alignment/DistanceCalculator.h
        PARENT_SCOPE
        )

set(alignment_source_files
        alignment/Alignment.cpp
        alignment/CompressedA3M.cpp
        alignment/Main.cpp
        alignment/Matcher.cpp
        alignment/MsaFilter.cpp
        alignment/MultipleAlignment.cpp
        alignment/PSSMCalculator.cpp
        alignment/StripedSmithWaterman.cpp
        alignment/BandedNucleotideAligner.cpp
        alignment/rescorediagonal.cpp
        PARENT_SCOPE
        )
